Research workbench
One rbd-up state of SARS-cov-2 D614G spike in complex with the SP1-77 neutralizing antibody Fab fragment
Analyse One rbd-up state of SARS-cov-2 D614G spike in complex with the SP1-77… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7UPY
- Type
- protein
- Length
- 4,619 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- UniProt
- P0DTC2
- Ligands
- NAG, MAN, FUC
Structure
electron microscopy · 5 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | — | protein | 1109 | — | P0DTC2 |
| B | — | protein | 1090 | — | P0DTC2 |
| C | — | protein | 1109 | — | P0DTC2 |
| H, D, F | — | protein | 225 | — | — |
| L, E, G | — | protein | 212 | — | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 91 copies · chains A, F, C, D, B, H
- MAN · alpha-D-mannopyranose · sugar · 12 copies
- FUC · alpha-L-fucopyranose · sugar · 6 copies · chains F, G, H, L, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Compared structures
- 7UPY · An antibody from single human VH-rearranging mouse neutralizes all SARS-CoV-2 variants… · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P0DTC2
- Elsewhere: RCSB PDB 7UPY · PDBe 7UPY · UniProt P0DTC2
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